Simon J. Puglisi

Simon J. Puglisi always looks tired these days Simon J. Puglisi used to live way down south
[Simon J. Puglisi used to live way down South.]
Academy of Finland Fellow
Department of Computer Science
University of Helsinki
P. O. Box 68
(Gustaf Hallstromin katu 2b)
email: puglisi [at] cs [.] helsinki [.] fi
office: A238, Kumpula Kampus
I'm an Academy of Finland Fellow at the University of Helsinki in the Department of Computer Science. I lead the Compressed Data Structures group (new website under construction), and am a member of the Genome Scale Algorithmics and the Practical Algorithms and Data Structures on Strings groups.

Prior to that I was a Newton Fellow in the Algorithms and Bioinformatics group at King's College London, and earlier still I held an Australian Postdoctoral Fellowship in the Search Engine Group at RMIT.

My current research focuses on efficient algorithms and data structures for searching, storing, and manipulating strings, trees and graphs, and applications thereof (like bioinformatics, information retrieval, database systems, and data mining).

I obtained my PhD from Curtin University, Western Australia, under the supervision of Bill Smyth and Andrew Turpin.

Selected (+ Recent) Publications

A fairly complete list is at DBLP. And then there is also Google Scholar.

Yasuo Tabei and Simon J. Puglisi. Scalable Similarity Search for Molecular Descriptors Proceedings of the 10th International Conference on Similarity Search and Applications (SISAP) (2017).

Juha Kärkkäinen, Marcin Piatowski, and Simon J. Puglisi. String Inference from Longest-Common-Prefix Arrays Proceedings of the 44th International Colloquium on Automata, Languages, and Programming (ICALP) (2017).

Juha Kärkkäinen, Dominik Kempa, Yuto Nakashima, Simon J. Puglisi, and Arseny Shur. On the Size of Lempel-Ziv and Lyndon Factorizations, Proceedings of the 34th International Symposium on Theoretical Aspects of Computer Science (STACS) (2017).

Andrea Poyias, Simon J. Puglisi, and Rajeev Raman. Compact Dynamic Rewritable (CDRW) Arrays, Proceedings of the Meeting on Algorithm Engineering and Experiments (ALENEX) (2017).

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi, and Bella Zhukova. Engineering External Memory Induced Suffix Sorting, Proceedings of the Meeting on Algorithm Engineering and Experiments (ALENEX) (2017).

Djamal Belazzougui and Simon J. Puglisi, Range Predecessor and Lempel-Ziv Parsing, Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA) (2016) [link to paper].

Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, and Simon J. Puglisi, Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices, Proceedings of the 22nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining (2016).

Djamal Belazzougui, Patrick Hagge Cording, Simon J. Puglisi, Yasuo Tabei, Access, Rank, and Select in Grammar-compressed Strings. Proceedings of the 23rd European Symposium on Algorithms (ESA) 2015, LNCS, 142-154 (2015).

Juha Kärkkäinen, Dominik Kempa, and Simon J. Puglisi, Parallel external memory suffix sorting, Proceedings of the 26th Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS, 329-342 (2015) [code].

Martin Muggli, Simon J. Puglisi, Roy Ronen, and Christina Boucher, Misassembly detection using paired-end sequence reads and optical mapping data. Bioinformatics 31(12): 80-88 (2015).

Dominik Kempa and Simon J. Puglisi, Lempel-Ziv factorization: fast, simple, practical, Proceedings of the Meeting on Algorithm Engineering and Experiments (ALENEX), SIAM, 103-112 (2013) [link to paper][code].

Research Activities

I am Associate Editor at the ACM Journal of Experimental Algorithmics.
I am helping to organise (with Hideo Bannai and Yasuo Tabei) String Masters in Tokyo, October 13, 16, and 17. Send me an email if you'd like to participate.
I am on the programme committee for ESA 2018, IWOCA 2018, and WALCOM 2018.
I was PC co-chair (with Rajeev Raman and Solon Pissis) of SEA 2017, held in wonderful London, June 21-23, 2017.
I was co-chair (with Yasuo Tabei) of WCTA 2016, which was a satellite to SPIRE in Japan.
I was PC co-chair (with Veli Mäkinen) of IWOCA 2016, which was held in Helsinki, August 17-19, 2016.
I was PC co-chair (with Emine Yilmaz and Costas Iliopoulos) of SPIRE 2015 in London in autumn 2015.
I was co-chair (with Costas Iliopoulos and Maxime Crochemore) of the Royal Society meeting on Storage and Indexing of Massive Data (here is a group photo).
I was co-Chair (with Golnaz Badkobeh) of the organizing committee for LSD 2012.
I was on the programme committee for CPM 2017, IWOCA 2017, CIBB 2017, SPIRE 2017, SPIRE 2016, CPM 2015, IWOCA 2015, SEA 2014, SPIRE 2014, SEA 2013, IWOCA 2013, SPIRE 2012, IWOCA 2012, CPM 2011, IWOCA 2011, IWOCA 2010, CIKM 2009, and SPIRE 2008.
I was on the organizing committee for CPM 2012 and SPIRE 2008.
I occasionally review papers for the following venues.


Bella Zhukova (PhD, U. Helsinki, current)
Joonas Nietosvaara (MSc, U. Helsinki, current)
Jussi Timonen (MSc, U. Helsinki, current)
Christopher Hoobin (PhD, RMIT, 2015, now at NASDAQ)
Jasbir Dhaliwal (PhD, RMIT, 2014, now at Monash U., formerly at IBM)
Alex Bowe (MSc, RMIT, 2013, now at Cruise Automation, PhD from U. Tokyo)
Shanika Kuruppu (PhD, U. Melbourne, 2013, now at Google)


With Juha Kärkkäinen, I ran the Data Compression seminar course in spring 2017.
I looked after the Combinatorial Pattern Matching seminar course in autumn 2015.
With Travis Gagie, I taught Data Compression Techniques in spring 2015.
With Travis Gagie and Juha Kärkkäinen, I looked after the Advanced Data Structures seminar course in autumn 2014.


I try to travel overseas as much as possible.
I enjoy listening to Arvo Part, Colleen, Boards of Canada, and various other music.
I love reading.
Science on the Edge.
The Long Now Foundation.
The Saws by Robert Pinsky.
First Idyll by Susan Stewart.
Next Door and I Took Out the Part by Jessica Greenbaum.
Solitaire by Deborah Landau.
On Friendship by Hagit Grossman.